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Allows to handle large datasets and produce highly contiguous and accurate assemblies within reasonable time. PE-Assembler is based on simple 3 extension approach and does not involve representing the entire genome in the form of a graph. Fundamentally, it is similar to other 3 extension approaches such as SSAKE, VCAKE and SHARCGS. However, it improves upon such early approaches in multiple ways. The extensive use of paired-end reads ensures that the dataset is localized within the region. Hence, this method can be run in parallel to greatly speedup the execution while staying within reasonable system requirements. Ambiguities are resolved using a multiple path extension approach, which takes into account sequence coverage, support from multiple paired libraries and more subtle information such as the span distribution of the paired-end reads.

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PE-Assembler classification

PE-Assembler specifications

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PE-Assembler distribution


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PE-Assembler support



  • Wing-Kin Sung <>


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Computational & Mathematical Biology Group, Genome Institute of Singapore, Singapore; School of Computing, National University of Singapore, Singapore

Funding source(s)

This research was supported by MOE AcRF Tier 2 funding R-252-000-444-112 and Agency for Science, Technology and Research (A*STAR).

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